LAMMPS (12 Jun 2025 - Development - patch_12Jun2025-584-g3e8807bee0-modified)
  using 1 OpenMP thread(s) per MPI task
units real
boundary p p p

atom_style full
bond_style harmonic
angle_style harmonic
special_bonds lj/coul 0.0 0.0 0.5

pair_style lj/cut/coul/long 12.0 12.0
kspace_style pppm 1.0e-3

comm_modify vel yes
read_data data.swm4-ndp
Reading data file ...
  orthogonal box = (-12 -12 -12) to (12 12 12)
  1 by 1 by 1 MPI processor grid
  reading atoms ...
  2500 atoms
  scanning bonds ...
  1 = max bonds/atom
  scanning angles ...
  1 = max angles/atom
  orthogonal box = (-12 -12 -12) to (12 12 12)
  1 by 1 by 1 MPI processor grid
  reading bonds ...
  2000 bonds
  reading angles ...
  500 angles
Finding 1-2 1-3 1-4 neighbors ...
  special bond factors lj:    0        0        0.5     
  special bond factors coul:  0        0        0.5     
     4 = max # of 1-2 neighbors
     3 = max # of 1-3 neighbors
     3 = max # of 1-4 neighbors
     4 = max # of special neighbors
  special bonds CPU = 0.000 seconds
  read_data CPU = 0.011 seconds

pair_coeff    1    1      0.210939     3.183950  # ODw ODw
pair_coeff    *   2*      0.000000     0.0

group ATOMS type 1:3
2000 atoms in group ATOMS
group CORES type 1
500 atoms in group CORES
group DRUDES type 4
500 atoms in group DRUDES

variable TK equal 300.0
variable TDK equal 1.0
variable PBAR equal 1.0

neighbor 2.0 bin

timestep 1.0

fix DRUDE all drude C N N D

velocity ATOMS create ${TK} 12345
velocity ATOMS create 300 12345
velocity DRUDES create ${TDK} 12345
velocity DRUDES create 1 12345

delete_bonds ATOMS multi
System init for delete_bonds ...
PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.21745695
  grid = 10 10 10
  stencil order = 5
  estimated absolute RMS force accuracy = 0.19728846
  estimated relative force accuracy = 0.00059412835
  using double precision FFTW3
  3d grid and FFT values/proc = 3375 1000
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Rebuild special list taking Drude particles into account
Old max number of 1-2 to 1-4 neighbors: 4
New max number of 1-2 to 1-4 neighbors: 4 (+0)
Neighbor list info ...
  update: every = 1 steps, delay = 0 steps, check = yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 14
  ghost atom cutoff = 14
  binsize = 7, bins = 4 4 4
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair lj/cut/coul/long, perpetual
      attributes: half, newton on
      pair build: half/bin/newton
      stencil: half/bin/3d
      bin: standard
Deleting bonds ...
  2000 total bonds, 500 turned on, 1500 turned off
  500 total angles, 0 turned on, 500 turned off
  0 total dihedrals, 0 turned on, 0 turned off
  0 total impropers, 0 turned on, 0 turned off

fix TEMP all langevin/drude ${TK} 100. 1256 ${TDK} 20. 13977 zero yes
fix TEMP all langevin/drude 300 100. 1256 ${TDK} 20. 13977 zero yes
fix TEMP all langevin/drude 300 100. 1256 1 20. 13977 zero yes
fix NPH ATOMS rigid/nph/small molecule iso ${PBAR} ${PBAR} 500.
fix NPH ATOMS rigid/nph/small molecule iso 1 ${PBAR} 500.
fix NPH ATOMS rigid/nph/small molecule iso 1 1 500.
Fix rigid/nph/small setup ...
  create bodies CPU = 0.000 seconds
  500 rigid bodies with 2000 atoms
  0.83209864 = max distance from body owner to body atom
fix NVE DRUDES nve

compute TEMP all temp/drude

thermo_style custom step etotal ke pe ebond eangle evdwl ecoul elong press vol temp c_TEMP[1] c_TEMP[2]
thermo 20

run 2000
PPPM initialization ...
  using 12-bit tables for long-range coulomb
  G vector (1/distance) = 0.21745695
  grid = 10 10 10
  stencil order = 5
  estimated absolute RMS force accuracy = 0.19728846
  estimated relative force accuracy = 0.00059412835
  using double precision FFTW3
  3d grid and FFT values/proc = 3375 1000
Generated 0 of 6 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 38.01 | 38.01 | 38.01 Mbytes
   Step         TotEng         KinEng         PotEng         E_bond        E_angle         E_vdwl         E_coul         E_long         Press          Volume          Temp        c_TEMP[1]      c_TEMP[2]   
         0   4568.0413      903.41148      3664.6298      623.46454      0              2890.2449      157955.66     -157804.74      244591.07      13824          202.18534      295.64644      14.858785    
        20   2882.3942      4527.6995     -1645.3053      561.7558       0              600.33719      155114.8      -157922.19      27167.649      14058.74       1013.3084      1438.6362      160.62623    
        40   1331.4572      3348.96       -2017.5028      681.45804      0              553.10287      154668.73     -157920.79      17927.382      14484.212      749.50412      1105.2128      36.587713    
        60   297.49703      2604.6292     -2307.1321      584.12796      0              409.12126      154634.45     -157934.83      13018.121      15026.562      582.92136      864.63163      18.334973    
        80  -373.92069      2264.123      -2638.0437      534.8037       0              212.33205      154542.73     -157927.91      6158.0414      15645.862      506.71538      755.71973      7.6932495    
       100  -905.84642      1912.267      -2818.1134      532.4086       0              87.506507      154496.6      -157934.63      2143.798       16288.813      427.96928      639.4619       4.128111     
       120  -1234.3628      1674.989      -2909.3518      544.9168       0              59.406245      154422.18     -157935.85      219.77626      16915.823      374.86598      560.50815      2.8318923    
       140  -1464.2319      1467.9588     -2932.1907      539.6024       0              41.234371      154424.96     -157937.99     -1497.843       17509.323      328.5322       491.4002       2.1391436    
       160  -1697.0946      1385.861      -3082.9556      553.58647      0              29.722767      154272.97     -157939.24     -3028.2649      18061.879      310.15853      463.9303       1.9946811    
       180  -1817.7957      1254.8843     -3072.68        560.4974       0              19.418696      154287.77     -157940.37     -3366.1123      18564.721      280.84569      420.14912      1.6771283    
       200  -1949.8327      1205.0473     -3154.8799      569.37428      0              15.882998      154200.77     -157940.91     -4087.1991      19014.132      269.69205      403.39324      1.7502928    
       220  -2031.0393      1152.1254     -3183.1646      597.72117      0              30.412845      154125.22     -157936.52     -4497.8409      19406.611      257.84802      385.67094      1.6864952    
       240  -2110.4136      1112.8207     -3223.2342      609.37252      0              60.515183      154048.84     -157941.97     -4376.2568      19739.029      249.05155      372.53682      1.5828975    
       260  -2190.0919      1076.0713     -3266.1632      611.90215      0              77.843723      153985.36     -157941.26     -4585.3546      20011.601      240.82697      360.23606      1.5271382    
       280  -2288.4254      1024.0481     -3312.4735      637.34832      0              126.3784       153863.71     -157939.91     -4492.3447      20225.53       229.18406      342.77605      1.5417241    
       300  -2352.323       1003.0185     -3355.3415      679.66666      0              171.42449      153734.49     -157940.92     -4115.3302      20382.729      224.47759      335.62404      1.7357363    
       320  -2414.5798      1014.79       -3429.3698      712.03346      0              208.85738      153590.97     -157941.23     -4297.4933      20486.591      227.11208      339.57297      1.7360731    
       340  -2441.5094      1045.42       -3486.9294      740.15798      0              263.25192      153449.26     -157939.59     -3878.6223      20539.028      233.96713      349.91188      1.6097103    
       360  -2501.1368      1055.1841     -3556.3209      772.80602      0              318.89393      153290.25     -157938.27     -3634.7061      20543.324      236.15237      353.09551      1.7937876    
       380  -2567.0541      1017.6691     -3584.7232      833.76295      0              414.09112      153106.38     -157938.96     -3088.4192      20504.931      227.75643      340.51309      1.7876055    
       400  -2646.8948      984.39779     -3631.2926      875.30807      0              457.12326      152975.88     -157939.6      -2840.1744      20430.027      220.31025      329.37336      1.7433927    
       420  -2672.7817      1050.4382     -3723.22        901.85913      0              467.84825      152846.05     -157938.98     -3026.9465      20322.09       235.09023      351.47759      1.8453386    
       440  -2725.4914      1027.076      -3752.5675      931.99605      0              519.25886      152732.77     -157936.59     -2658.7834      20181.55       229.86172      343.68392      1.7575912    
       460  -2756.4341      1005.3232     -3761.7573      965.50219      0              575.44376      152636.97     -157939.67     -2339.6778      20013.467      224.9934       336.4094       1.711424     
       480  -2806.6793      1011.4832     -3818.1625      997.21383      0              615.8086       152510.55     -157941.73     -1850.7939      19823.789      226.37202      338.38581      1.8917064    
       500  -2870.0549      1004.8393     -3874.8942      1022.583       0              621.43418      152423.47     -157942.38     -1887.6347      19615.768      224.8851       336.25668      1.6921641    
       520  -2938.9032      986.49197     -3925.3952      1053.5148      0              663.30758      152298.46     -157940.67     -2135.9206      19390.333      220.77893      330.0916       1.7120314    
       540  -2996.4427      1009.5946     -4006.0374      1087.5002      0              678.20794      152167.24     -157938.99     -1997.6419      19150.156      225.94935      337.79402      1.8081169    
       560  -3043.5142      1018.9636     -4062.4778      1143.7459      0              754.81602      151980.18     -157941.22     -1668.5286      18897.283      228.04615      340.90677      1.8688188    
       580  -3072.6645      1013.4714     -4086.136       1177.0429      0              816.92128      151861.3      -157941.4      -762.07188      18638.563      226.81699      339.06462      1.8680917    
       600  -3129.932       1018.1959     -4148.1278      1180.3522      0              809.1813       151804.89     -157942.55     -1213.1966      18380.41       227.87432      340.69063      1.7859603    
       620  -3154.7179      1005.2601     -4159.978       1206.5557      0              854.68809      151722.78     -157944        -569.71583      18123.773      224.97928      336.36252      1.7628276    
       640  -3168.1013      1049.2357     -4217.337       1244.6888      0              919.88059      151561.72     -157943.63     -72.063076      17872.876      234.8211       351.02659      1.9404974    
       660  -3193.4813      1032.9221     -4226.4034      1246.3615      0              909.08968      151562.87     -157944.73      165.53034      17632.095      231.17008      345.54214      1.9636239    
       680  -3251.5826      1029.5803     -4281.1628      1286.6126      0              953.58543      151422.26     -157943.62      572.88422      17402.757      230.42218      344.47192      1.8618611    
       700  -3308.0025      1001.7058     -4309.7083      1288.7461      0              989.10938      151354.33     -157941.89      859.15045      17186.114      224.18382      335.06073      1.9816429    
       720  -3356.0882      994.49894     -4350.5871      1332.1117      0              1009.6402      151252.5      -157944.84      790.50788      16984.824      222.57091      332.70615      1.8552779    
       740  -3383.1476      978.84499     -4361.9926      1355.1986      0              1036.0497      151190.16     -157943.41      1211.7454      16798.13       219.06752      327.39963      1.9651581    
       760  -3414.129       974.58355     -4388.7125      1350.4824      0              1002.1619      151202.43     -157943.78      1023.2926      16626.692      218.1138       326.00321      1.8987495    
       780  -3428.0249      960.09477     -4388.1197      1329.3261      0              993.5851       151231.99     -157943.02      847.84664      16468.871      214.87118      321.16351      1.8567749    
       800  -3495.9217      958.87055     -4454.7922      1361.3865      0              1000.4352      151125.36     -157941.97      757.18852      16323.04       214.5972       320.70092      1.9605634    
       820  -3544.4465      935.57427     -4480.0208      1346.8738      0              954.06846      151162.19     -157943.16      164.56805      16187.495      209.38344      312.90962      1.9123083    
       840  -3569.6132      932.18923     -4501.8024      1333.2307      0              956.55179      151154.44     -157946.03      329.3056       16058.215      208.62586      311.69043      2.0794775    
       860  -3585.6773      939.74807     -4525.4254      1368.2448      0              982.68312      151068.32     -157944.67      566.66129      15935.3        210.31755      314.30658      1.9188485    
       880  -3611.4588      943.84279     -4555.3015      1416.8124      0              1020.9961      150950.9      -157944.01      754.61389      15820.235      211.23395      315.6253       2.028804     
       900  -3639.7854      931.58647     -4571.3719      1418.887       0              1067.4844      150886.19     -157943.93      1448.4741      15714.741      208.49096      311.54855      1.9588195    
       920  -3646.5856      922.59998     -4569.1856      1439.6673      0              1110.897       150825.9      -157945.65      2258.4485      15622.291      206.47977      308.53728      1.9517875    
       940  -3680.9374      952.07648     -4633.0139      1435.8332      0              1065.7874      150808.75     -157943.38      1039.311       15545.937      213.07667      318.41516      1.9735461    
       960  -3683.2842      938.4368      -4621.721       1440.0689      0              1052.2075      150831.06     -157945.06      1162.2701      15480.775      210.02408      313.79386      2.0644713    
       980  -3699.1821      900.22313     -4599.4052      1429.9355      0              1086.078       150830.27     -157945.69      1691.1313      15425.384      201.47178      301.03001      1.952396     
      1000  -3697.2026      936.25525     -4633.4579      1416.1344      0              1062.0042      150833.87     -157945.47      1270.2897      15381.509      209.53585      313.09229      2.0038814    
      1020  -3732.4456      944.86982     -4677.3155      1434.1732      0              1043.6235      150790.57     -157945.68      1001.4551      15347.626      211.4638       316.03161      1.9052674    
      1040  -3734.9912      947.61399     -4682.6052      1448.26        0              1036.682       150779.06     -157946.61      579.60601      15321.269      212.07796      316.90543      1.9988537    
      1060  -3704.4142      965.84857     -4670.2628      1466.7234      0              1036.1925      150773.51     -157946.69      668.66193      15300.428      216.15889      323.00554      2.0332872    
      1080  -3739.1176      930.45576     -4669.5733      1473.5922      0              1077.8388      150725.45     -157946.45      1301.2171      15284.87       208.23791      311.15156      1.9941209    
      1100  -3735.0376      920.84596     -4655.8836      1478.435       0              1090.0602      150721.25     -157945.62      1452.1613      15278.337      206.08722      307.86211      2.1252647    
      1120  -3734.0462      931.43783     -4665.484       1468.4826      0              1048.6317      150764.3      -157946.9       1057.6351      15282.153      208.4577       311.48338      1.9894204    
      1140  -3760.8373      902.12317     -4662.9605      1449.2253      0              1029.1746      150805.86     -157947.22      1000.2749      15293.375      201.89702      301.71407      1.8591169    
      1160  -3760.7722      936.58594     -4697.3582      1464.4657      0              1046.0596      150736.68     -157944.57      794.70861      15309.724      209.60986      313.19799      2.0143735    
      1180  -3760.4099      950.29015     -4710.7         1496.4397      0              1072.3441      150667.12     -157946.6       972.87915      15330.426      212.67689      317.81796      1.9693909    
      1200  -3783.9078      920.48835     -4704.3962      1526.0856      0              1109.2049      150605.93     -157945.62      1164.4426      15357.27       206.00718      307.80984      1.9898583    
      1220  -3785.8602      909.55882     -4695.419       1529.8648      0              1091.0654      150629.41     -157945.76      779.4137       15390.602      203.56113      304.08746      2.1013549    
      1240  -3781.5323      900.70029     -4682.2326      1500.0432      0              1084.9348      150678.64     -157945.86      934.62414      15428.315      201.57857      301.11462      2.1033311    
      1260  -3789.2144      911.79548     -4701.0099      1482.8158      0              1031.0689      150732.12     -157947.02      108.66101      15471.541      204.0617       304.84201      2.0929459    
      1280  -3779.3303      922.25347     -4701.5838      1445.2796      0              982.61129      150817.28     -157946.76     -91.644595      15515.828      206.40222      308.41282      1.9682119    
      1300  -3778.9223      897.68441     -4676.6067      1423.0802      0              956.27459      150889.27     -157945.23     -449.97692      15558.128      200.90361      300.19882      1.9113863    
      1320  -3772.4998      878.70097     -4651.2007      1428.3429      0              983.0807       150883.54     -157946.17     -348.57709      15597.02       196.65508      293.83559      1.9007518    
      1340  -3782.7602      894.75449     -4677.5147      1431.7862      0              973.822        150863.97     -157947.09     -500.43428      15632.832      200.24789      299.24932      1.8445387    
      1360  -3814.0604      889.7205      -4703.7809      1431.6897      0              951.05306      150859.94     -157946.47     -951.55641      15664.625      199.12127      297.45709      2.0513934    
      1380  -3789.5032      892.3251      -4681.8283      1429.1282      0              961.5751       150873.29     -157945.82     -1088.7805      15689.946      199.70419      298.34776      2.0176464    
      1400  -3759.7741      935.96888     -4695.743       1468.2212      0              970.05416      150811.87     -157945.89     -1322.5585      15708.325      209.47176      313.02234      1.9516506    
      1420  -3750.9996      919.15309     -4670.1527      1437.5563      0              944.81448      150893.46     -157945.99     -968.98867      15719.716      205.70835      307.36116      1.9913077    
      1440  -3761.4324      882.17812     -4643.6105      1406.6888      0              922.75634      150972.52     -157945.58     -1048.2184      15724.271      197.43327      294.98303      1.938889     
      1460  -3742.6306      936.03501     -4678.6656      1424.851       0              940.00062      150902.69     -157946.21     -1004.033       15721.308      209.48656      313.02329      1.9941159    
      1480  -3776.4606      900.82088     -4677.2815      1448.2346      0              969.1092       150849.54     -157944.17     -1104.6042      15711.458      201.60556      301.2316       1.95027      
      1500  -3787.1671      918.0609      -4705.2281      1451.4715      0              960.42402      150829.69     -157946.81     -1168.0909      15695.778      205.46391      307.01001      1.9607908    
      1520  -3815.0411      891.83084     -4706.872       1466.3431      0              962.62677      150810.83     -157946.67     -807.73446      15673.565      199.59357      298.23287      1.9157993    
      1540  -3804.4958      904.9226      -4709.4184      1461.9726      0              964.64137      150809.83     -157945.86     -981.4341       15644.878      202.52354      302.66651      1.8325485    
      1560  -3788.9762      916.40204     -4705.3782      1466.3412      0              1000.9824      150773.14     -157945.84     -757.69187      15609.714      205.09266      306.48965      1.8884801    
      1580  -3788.5072      910.97904     -4699.4862      1471.624       0              1029.0524      150746.35     -157946.52     -24.362802      15570.752      203.87898      304.60245      2.0242746    
      1600  -3830.5491      879.75648     -4710.3056      1482.7485      0              1045.6243      150706.87     -157945.54      226.67098      15531.671      196.89131      294.14962      1.9808847    
      1620  -3867.9675      887.94607     -4755.9136      1499.4036      0              1056.3273      150635.19     -157946.83      166.79224      15493.07       198.72415      296.94545      1.8841031    
      1640  -3855.0225      890.35893     -4745.3815      1505.2568      0              1076.0604      150618.7      -157945.4       536.6886       15455.059      199.26416      297.70164      1.990654     
      1660  -3881.5508      891.97071     -4773.5215      1527.413       0              1092.0758      150553.07     -157946.08      564.43904      15418.874      199.62488      298.30432      1.8667293    
      1680  -3864.2712      906.17587     -4770.4471      1572.9057      0              1137.8747      150465.39     -157946.62      895.77232      15386.24       202.80402      303.03286      1.9407316    
      1700  -3886.1705      890.67426     -4776.8448      1584.8017      0              1185.1221      150399.81     -157946.57      1309.3367      15360.857      199.33473      297.77126      2.0629827    
      1720  -3846.2753      931.91345     -4778.1887      1583.5497      0              1187.2123      150397.19     -157946.14      1659.042       15345.483      208.56414      311.62126      2.0327758    
      1740  -3860.134       923.82317     -4783.9571      1616.4386      0              1227.5033      150318.84     -157946.74      2364.4345      15340.773      206.75352      308.90192      2.043215     
      1760  -3889.5294      906.03746     -4795.5668      1588.2734      0              1226.8617      150334.61     -157945.31      1495.6061      15349.158      202.77304      302.98151      1.9505596    
      1780  -3902.2198      905.11997     -4807.3398      1581.1944      0              1186.3438      150372.64     -157947.52      1577.5526      15370.313      202.56771      302.71557      1.866847     
      1800  -3932.0824      873.19271     -4805.2751      1536.1311      0              1116.1089      150488.49     -157946.01      833.30702      15400.131      195.42232      291.959        1.9581112    
      1820  -3914.1206      876.13262     -4790.2532      1508.2896      0              1081.2509      150567.29     -157947.08     -7.1622984      15433.581      196.08028      292.95492      1.9388434    
      1840  -3915.47        884.79674     -4800.2668      1533.4392      0              1063.1724      150549.21     -157946.09     -234.2528       15467.808      198.01933      295.87137      1.9192092    
      1860  -3929.8818      876.76793     -4806.6497      1535.235       0              1080.817       150523.47     -157946.17     -167.03732      15501.326      196.22246      293.13775      1.9994389    
      1880  -3930.7209      868.03007     -4798.751       1537.8523      0              1074.6742      150535.2      -157946.48     -209.98725      15534.478      194.26691      290.26839      1.8754099    
      1900  -3904.2922      884.22488     -4788.5171      1515.2746      0              1050.1528      150591.02     -157944.97     -565.38571      15565.576      197.89134      295.65618      1.9658861    
      1920  -3906.3469      893.03246     -4799.3794      1503.8085      0              1006.6027      150636.5      -157946.29     -1192.5374      15592.505      199.8625       298.61026      1.9672386    
      1940  -3882.8991      870.46824     -4753.3673      1484.6896      0              1017.0257      150691.4      -157946.48     -604.0552       15614.175      194.81258      291.08512      1.8778712    
      1960  -3863.4136      914.31078     -4777.7244      1471.0035      0              1013.3739      150683.03     -157945.13     -735.68569      15631.041      204.62463      305.82893      1.8067693    
      1980  -3870.832       944.18837     -4815.0203      1515.91        0              1050.1054      150565.6      -157946.64     -641.8275       15643.24       211.31129      315.76603      1.979206     
      2000  -3858.7185      877.07277     -4735.7912      1508.6523      0              1083.653       150617.95     -157946.05      156.65905      15653.338      196.29069      293.12854      2.2223895    
Loop time of 38.9584 on 1 procs for 2000 steps with 2500 atoms

Performance: 4.436 ns/day, 5.411 hours/ns, 51.337 timesteps/s, 128.342 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 33.383     | 33.383     | 33.383     |   0.0 | 85.69
Bond    | 0.010626   | 0.010626   | 0.010626   |   0.0 |  0.03
Kspace  | 0.91652    | 0.91652    | 0.91652    |   0.0 |  2.35
Neigh   | 3.0081     | 3.0081     | 3.0081     |   0.0 |  7.72
Comm    | 0.23732    | 0.23732    | 0.23732    |   0.0 |  0.61
Output  | 0.0036977  | 0.0036977  | 0.0036977  |   0.0 |  0.01
Modify  | 1.3736     | 1.3736     | 1.3736     |   0.0 |  3.53
Other   |            | 0.02585    |            |       |  0.07

Nlocal:           2500 ave        2500 max        2500 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:          21225 ave       21225 max       21225 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:    2.29344e+06 ave 2.29344e+06 max 2.29344e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 2293445
Ave neighs/atom = 917.378
Ave special neighs/atom = 4
Neighbor list builds = 102
Dangerous builds = 0

Total wall time: 0:00:39
